Recent findings from the human proteome project: opening the mass spectrometry toolbox to advance cancer diagnosis, surveillance and treatment

Cantor, David; Nice, Edouard C.; Baker, Mark S.

doi:10.1586/14789450.2015.1040770

Cited by 18 publications

(11 citation statements)

References 115 publications

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“…Cancer development is an extremely complex and heterogeneous event, making it a challenging task to elucidate key effectors among numerous putative factors in a reasonable time frame. However, recent rapid advances in proteomic technologies are facilitating the analysis of protein signaling pathways in a high‐throughput manner , which is greatly accelerating biomarker discovery and revolutionizing the landscape for disease treatment and diagnosis . Initiatives such as those recently emanating from multidisciplinary teams (e.g., ) have enabled very deep profiling of clinical samples with high identification and quantification accuracy, allowing the identification of several disease proteomes (e.g., breast, ovary, and colon).…”

Section: Resultsmentioning

confidence: 99%

Proteomic profiling of human plasma for cancer biomarker discovery

Huang

et al. 2016

Proteomics

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Over the past decades, substantial advances have been made in both the early diagnosis and accurate prognosis of many cancers because of the impressive development of novel proteomic strategies. However, it remains difficult to standardize proteomic approaches. In addition, the heterogeneity of proteins in distinct tissues results in incomplete population of the whole proteome, which inevitably limits its clinical practice. As one of the most complex proteomes in the human body, the plasma proteome contains secreted proteins originating from multiple organs and tissues, making it a favorable matrix for comprehensive biomarker discovery. Here, we will discuss the roles of plasma proteome profiling in cancer biomarker discovery and validation, and highlight both the inherent advantages and disadvantages. Although several hurdles lay ahead, further advances in this technology will greatly increase our understanding of cancer biology, reveal new biomarkers and biomarker panels, and open a new avenue for more efficient early diagnosis and surveillance of cancer, leading toward personalized medicine.

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Section: Resultsmentioning

confidence: 99%

Proteomic profiling of human plasma for cancer biomarker discovery

Huang

et al. 2016

Proteomics

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“…The most clinically relevant and therefore ideal output from proteomics research is obviously the reliable identification and quantification of cancer surrogate endpoints (i.e., biomarkers validated to predict clinical outcome in an accurate and reproducible manner) in easily accessible patient biofluids, such as plasma, serum, saliva, tears, urine, or feces ( 160 , 161 ). In reality, different kinds of molecular targets have been used to discover biomarkers in blood/plasma/serum, body fluids, tissues, and their secretions ( 162 ).…”

Section: Targeted Proteomics In Cancermentioning

confidence: 99%

A Timely Shift from Shotgun to Targeted Proteomics and How It Can Be Groundbreaking for Cancer Research

et al. 2017

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The fact that cancer is a leading cause of death all around the world has naturally sparked major efforts in the pursuit of novel and more efficient biomarkers that could better serve as diagnostic tools, prognostic predictors, or therapeutical targets in the battle against this type of disease. Mass spectrometry-based proteomics has proven itself as a robust and logical alternative to the immuno-based methods that once dominated the field. Nevertheless, intrinsic limitations of classic proteomic approaches such as the natural gap between shotgun discovery-based methods and clinically applicable results have called for the implementation of more direct, hypothesis-based studies such as those made available through targeted approaches, that might be able to streamline biomarker discovery and validation as a means to increase survivability of affected patients. In fact, the paradigm shifting potential of modern targeted proteomics applied to cancer research can be demonstrated by the large number of advancements and increasing examples of new and more useful biomarkers found during the course of this review in different aspects of cancer research. Out of the many studies dedicated to cancer biomarker discovery, we were able to devise some clear trends, such as the fact that breast cancer is the most common type of tumor studied and that most of the research for any given type of cancer is focused on the discovery diagnostic biomarkers, with the exception of those that rely on samples other than plasma and serum, which are generally aimed toward prognostic markers. Interestingly, the most common type of targeted approach is based on stable isotope dilution-selected reaction monitoring protocols for quantification of the target molecules. Overall, this reinforces that notion that targeted proteomics has already started to fulfill its role as a groundbreaking strategy that may enable researchers to catapult the number of viable, effective, and validated biomarkers in cancer clinical practice.

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“…Knowledge and technical resources generated within the C-HPP initiative are expected to contribute to progress in the understanding and treatment of diseases by the integration and coordination of specific research initiatives through the Biology and Disease (BD)–HPP initiative [ 20 ]. Among the 23 BD initiatives currently active, recent developments in cancer proteomics have been summarized highlighting the impressive contribution that the mass spectrometry tool box is already making to reduce the global burden of this disease [ 21 ].…”

Section: Introductionmentioning

confidence: 99%

In-Depth Proteomic Characterization of Classical and Non-Classical Monocyte Subsets

et al. 2018

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Monocytes are bone marrow-derived leukocytes that are part of the innate immune system. Monocytes are divided into three subsets: classical, intermediate and non-classical, which can be differentiated by their expression of some surface antigens, mainly CD14 and CD16. These cells are key players in the inflammation process underlying the mechanism of many diseases. Thus, the molecular characterization of these cells may provide very useful information for understanding their biology in health and disease. We performed a multicentric proteomic study with pure classical and non-classical populations derived from 12 healthy donors. The robust workflow used provided reproducible results among the five participating laboratories. Over 5000 proteins were identified, and about half of them were quantified using a spectral counting approach. The results represent the protein abundance catalogue of pure classical and enriched non-classical blood peripheral monocytes, and could serve as a reference dataset of the healthy population. The functional analysis of the differences between cell subsets supports the consensus roles assigned to human monocytes.

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Recent findings from the human proteome project: opening the mass spectrometry toolbox to advance cancer diagnosis, surveillance and treatment

Cited by 18 publications

References 115 publications

Proteomic profiling of human plasma for cancer biomarker discovery

Proteomic profiling of human plasma for cancer biomarker discovery

A Timely Shift from Shotgun to Targeted Proteomics and How It Can Be Groundbreaking for Cancer Research

In-Depth Proteomic Characterization of Classical and Non-Classical Monocyte Subsets

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